It will definitely not work well together, however with the beta version of SFC you can simply add an fb:comments tag to your theme to make the Facebook Comments box show up on the site.
Beta version of SFC is here.
http://plugins.svn.wordpress.org/simple-facebook-connect/branches/new-sfc/
The comments tag you add would look something like this:
<fb:comments href="<?php the_permalink()?>" num_posts="10" width="500"></fb:comments>
